SchemaUsageReport is not visiting applied directives #3267

Describe the bug
SchemaUsageReport is not visiting GraphQLAppliedDirectives, this can sometimes result in SchemaUsage giving incorrect information about whether a directive is being referenced.

To Reproduce

• create a schema that contains a directive definition and a field that uses that directive
• manipulate the schema, clearing the list of directives from the field, and adding the applied directive back to it.
  For example:

List<GraphQLAppliedDirectives> directives = fieldDef.getAppliedDirectives();
fieldDef.transform(f -> f.clearDirectives().replaceAppliedDirectives(directives))

• at this point the field should have an empty list of GraphQLDirective, and a list of GraphQLAppliedDirective containing 1 item
• run the schema through SchemaUsage and check if the directive is being referenced:

schemaUsage.isStronglyReferenced(schema, "directiveName")

expected behaviour: isStronglyReferenced should return true, since the directive is applied to the field
actual behaviour: isStronglyReferenced returns false